X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 277.0
Details well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.32 α = 90
b = 90.32 β = 90
c = 106.72 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2016-09-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.77 63.09 99.7 0.046 -- -- -- -- 94504 -- -3.0 36.58
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.77 1.88 99.8 1.154 -- 1.0 -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.771 63.091 -- 1.33 -- 49189 1934 99.45 -- 0.2037 0.2027 0.2285 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.7709 1.8151 -- 142 3301 0.3469 0.3572 -- 100.0
X Ray Diffraction 1.8151 1.8642 -- 128 3394 0.3135 0.2938 -- 100.0
X Ray Diffraction 1.8642 1.9191 -- 145 3317 0.2778 0.3405 -- 100.0
X Ray Diffraction 1.9191 1.981 -- 128 3259 0.3678 0.3951 -- 97.0
X Ray Diffraction 1.981 2.0518 -- 135 3358 0.252 0.2754 -- 100.0
X Ray Diffraction 2.0518 2.134 -- 138 3351 0.242 0.2993 -- 100.0
X Ray Diffraction 2.134 2.2311 -- 141 3355 0.223 0.2972 -- 100.0
X Ray Diffraction 2.2311 2.3487 -- 136 3250 0.266 0.2863 -- 97.0
X Ray Diffraction 2.3487 2.4959 -- 136 3423 0.2081 0.2624 -- 100.0
X Ray Diffraction 2.4959 2.6886 -- 145 3374 0.2017 0.2106 -- 100.0
X Ray Diffraction 2.6886 2.9592 -- 139 3400 0.2008 0.2114 -- 100.0
X Ray Diffraction 2.9592 3.3874 -- 136 3422 0.1989 0.1956 -- 100.0
X Ray Diffraction 3.3874 4.2676 -- 140 3465 0.1767 0.2104 -- 100.0
X Ray Diffraction 4.2676 63.1308 -- 145 3586 0.1756 0.2031 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 50.0446
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.2
f_plane_restr 0.015
f_angle_d 2.414
f_bond_d 0.031
f_dihedral_angle_d 20.155
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2309
Nucleic Acid Atoms 0
Heterogen Atoms 78
Solvent Atoms 191

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10.1_2155
XSCALE data scaling
PHASER phasing
PDB_EXTRACT data extraction version: 3.22
XDS data reduction